plotNormalizedData           package:CALIB           R Documentation

_p_l_o_t _e_s_t_i_m_a_t_e_d _a_b_s_o_l_u_t_e _l_e_v_e_l_s _o_f _t_w_o _c_o_n_d_i_t_i_o_n_s

_D_e_s_c_r_i_p_t_i_o_n:

     plot estimated absolute levels of any two user-specified
     conditions. The values in the plot are in log scale.

_U_s_a_g_e:

     plotNormalizedData(data, condition = c(1, 2), xlab = NULL, ylab = NULL,
                        main = NULL,xlim = NULL, ylim = NULL, pch = 19,
                        cex = 0.2,col = "black", diag=TRUE, diagcol="blue",
                        diaglwd=1.5, ...)

_A_r_g_u_m_e_n_t_s:

    data: matrix containing estimated absolute levels. columns are
          conditons and rows are genes.

condition: integer vector giving the two conditions to be plotted.

    xlab: a title for the x axis.

    ylab: a title for the y axis.

    main: an overall title for the plot. 

    xlim: the x limits (min,max) of the plot.

    ylim: the y limits of the plot.

     pch: an integer code for one of a set of plotting characters  or
          symbols for the spike data set. Default is 19.

     cex: a numerical value giving the amount by which points should be
          scaled relative to the default. Default is 0.2.

     col: the color of the points. Default is black.

    diag: a logical value. Add diagonal on the plot if it is 'TRUE'. 
          Default is 'TRUE'.

 diagcol: the color of the diagonal. Default is blue.

 diaglwd: the width of the diagonal. Default is 1.5.

     ...: other graphical parameters can be used in function 'plot'. 

_D_e_t_a_i_l_s:

     The function polts estimated absolute expression levels of two
     conditions. It accepts expression levels from the argument 'data',
     which should have the same data format as  the output value of the
     function 'NormalizeData'.

     The two conditions to be plotted should be specified by the
     argument 'condition'.  The 'condition' should be a numeric vector
     with length two and it should be subset of condition vector of the
     design matrix. see function 'NormalizeData'.

     see other graphic functions for the other arguments.

_V_a_l_u_e:

     A plot is created on the current graphics device.

_A_u_t_h_o_r(_s):

     Hui Zhao

_E_x_a_m_p_l_e_s:

     # load data: normalized data
     data(normdata)
             
     # specify the two conditions to be plotted.
     cond <- c(1,2)
             
     # use the default values for other parameters.
     plotNormalizedData(normdata,condition = cond)

